suppressMessages(library(ArchR))
library(parallel)
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=18, repr.plot.height=13)
suppressMessages(library(Seurat))
suppressMessages(library(SingleCellExperiment))
library(tidyverse)
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 8)
##################################
### load mm ArchR genome ###
addArchRGenome('mm10')
Input threads is equal to or greater than ncores minus 1 (7) Setting cores to ncores minus 2. Set force = TRUE to set above this number! Setting default number of Parallel threads to 6. Setting default genome to Mm10.
PROJDIR='../../../data/tidy_data/ArchRProjects'
proj = loadArchRProject(file.path(PROJDIR,'Mouse_DorsalHorn_scATAC'), showLogo = FALSE)
projNeuron = loadArchRProject(file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_neuron2'), showLogo = FALSE) #neuron2 is correct proj
projGlia = loadArchRProject(file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_glia'), showLogo = FALSE)
Successfully loaded ArchRProject! Successfully loaded ArchRProject! Successfully loaded ArchRProject!
proj
projNeuron
projGlia
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ... Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(31): Sample TSSEnrichment ... predictedGroup_RNA2ATAC FINAL_GROUP_LABEL numberOfCells(1): 75955 medianTSS(1): 23.946 medianFrags(1): 16376
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_neuron2 samples(12): Mouse_DH_SEA2253A60 Mouse_DH_SEA2253A61 ... Mouse_DH_SEA2253A69 Mouse_DH_SEA2253A68 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(40): Sample TSSEnrichment ... predictedScore_RNA2ATAC_clustertype FINAL_GROUP_LABEL numberOfCells(1): 20591 medianTSS(1): 20.626 medianFrags(1): 25740
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_glia samples(12): Mouse_DH_SEA2253A61 Mouse_DH_SEA2253A60 ... Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A64 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(38): Sample TSSEnrichment ... Clusters_RNALabels FINAL_GROUP_LABEL numberOfCells(1): 55364 medianTSS(1): 25.181 medianFrags(1): 14350
#we need to standardize the column names, and choose the ones we want to keep
(names(getCellColData(projNeuron)))
(names(getCellColData(projGlia)))
#explain why each column is being dropped
#NEURONS
drop <- c("predictedCell_Co", "predictedGroup_RNA2ATACCo", "predictedScore_RNA2ATACCo", "predictedCell_Co_cell",
"predictedGroup_RNA2ATACCo_cell", "predictedScore_RNA2ATACCo_cell", "Neuron_Type")
Neur_vec <- names(getCellColData(projNeuron))
Neur_vec <- Neur_vec[Neur_vec %ni% drop]
df_Neuron = getCellColData(projNeuron, select = Neur_vec) #Neuron_type was manual annotations that aren't relevant anymore
#Set integrated labels as predictedXXXX_RNA2ATAC
colnames(df_Neuron)[which(names(df_Neuron) == "predictedCell_clustertype")] <- "predictedCell_RNA2ATAC"
colnames(df_Neuron)[which(names(df_Neuron) == "predictedGroup_RNA2ATAC_clustertype")] <- "predictedGroup_RNA2ATAC"
colnames(df_Neuron)[which(names(df_Neuron) == "predictedScore_RNA2ATAC_clustertype")] <- "predictedScore_RNA2ATAC"
names(df_Neuron)
#GLIA
drop = c("ClustersX10_tmp",'ClustersX10','ClustersX20','ClustersX30','ClustersX40','ClustersX50')
Glia_vec <- names(getCellColData(projGlia))
Glia_vec <- Glia_vec[Glia_vec %ni% drop]
Glia_vec #names of columns we want to keep
df_Glia = getCellColData(projGlia, select = Glia_vec)
#REPLACE predictedXXXX_RNA2ATAC WITH CLUSTERS_RNALABELS
df_Glia$predictedGroup_RNA2ATACCo = df_Glia$Clusters_RNALabels
df_Glia = df_Glia[,-31]
colnames(df_Glia)[which(names(df_Glia) == "predictedCell_Co")] <- "predictedCell_RNA2ATAC"
colnames(df_Glia)[which(names(df_Glia) == "predictedGroup_RNA2ATACCo")] <- "predictedGroup_RNA2ATAC"
colnames(df_Glia)[which(names(df_Glia) == "predictedScore_RNA2ATACCo")] <- "predictedScore_RNA2ATAC"
names(df_Glia)
table(df_Glia$Celltype1)
table(df_Glia$predictedGroup_RNA2ATAC)
Astrocyte Meninges Micro Oligo OPC Schwann
13355 603 3284 33256 781 4085
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells Meninges
2417 10926 788 951 2
Microglia Mural Oligo.1 Oligo.2 OPC
2328 736 32624 1244 3348
Glia_columns = names(df_Glia)
Neuron_columns = names(df_Neuron)
Neuron_columns
Glia_columns
table(df_Neuron$predictedGroup_RNA2ATAC)
table(df_Glia$predictedGroup_RNA2ATAC)
GABA1 GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2 GABA5 GLUT1 GLUT10 GLUT11 1078 64 1545 376 967 795 1320 1092 431 39 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 midVen 2452 1945 341 992 2195 2283 1157 1 1518
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells Meninges
2417 10926 788 951 2
Microglia Mural Oligo.1 Oligo.2 OPC
2328 736 32624 1244 3348
#check to see if this merge is working properly
columns = names(df_Glia)
df_label = rbind(df_Neuron[,columns],df_Glia[,columns] )
df_label
dim(df_label)
print(getCellColData(proj))
DataFrame with 75955 rows and 30 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse_DH_SEA2253A58 18.201
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69 10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69 17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69 11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69 13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69 30.716
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 7445 25859
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 243 1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 446 1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 283 1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 318 1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 667 2131
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 5408 0.183335 1
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 138 0.156816 1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 268 0.235505 1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 208 0.194057 1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 164 0.192780 1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 170 0.332449 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.883453 5368 37444
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 9.203030 721 330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.428157 438 1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 4.676420 681 581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 7.410853 707 387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.510368 150 2122
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 70524 27712 0
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 3367 2316 0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 3346 1530 0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 3298 2036 0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 3255 2161 0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 3205 933 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.5666667 0.0383416
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.2444444 0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.0222222 0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.0000000 0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.3555556 0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.6444444 0.0265211
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse DorsalHorn C9
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse DorsalHorn C24
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 EXC
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 EXC
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 EXC
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 EXC
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C11 4.84834 EXC
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C24 3.52724 Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C1 3.52453 Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C1 3.51825 Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C24 3.51255 Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C24 3.50583 Oligo
ClustersX60 predictedCell_RNA2ATAC
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C6 877
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C9 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C12 1303
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C10 8064
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C16 4865
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C16 9822
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C20 6548
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C20 10602
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C16 9822
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C19 2160
predictedGroup_RNA2ATAC
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC midVen
... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1
predictedScore_RNA2ATAC
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 1.000000
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.948107
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.850651
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.408128
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.475185
... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.925414
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.000000
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.981841
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.968747
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.860995
DataFrame with 75955 rows and 29 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58 25.310
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69 10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69 17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69 11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69 13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69 30.716
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 13881 45719
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 243 1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 446 1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 283 1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 318 1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 667 2131
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 3927 0.314804 1
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 138 0.156816 1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 268 0.235505 1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 208 0.194057 1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 164 0.192780 1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 170 0.332449 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.627884 6400 44607
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 9.203030 721 330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.428157 438 1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 4.676420 681 581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 7.410853 707 387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.510368 150 2122
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 72615 21608 0
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 3367 2316 0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 3346 1530 0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 3298 2036 0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 3255 2161 0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 3205 933 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.7666667 0.0270399
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.2444444 0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.0222222 0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.0000000 0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.3555556 0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.6444444 0.0265211
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse DorsalHorn C20
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse DorsalHorn C24
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC C20 4.86103 Micro
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C24 3.52724 Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C1 3.52453 Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C1 3.51825 Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C24 3.51255 Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C24 3.50583 Oligo
predictedGroup_RNA2ATACCo ReadsInPeaks
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen 63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen 67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1 52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen 66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Ependymal.cells 98301
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1 2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia 3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia 2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1 3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1 4068
FRIP
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.398623
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.456443
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.356678
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.457930
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.676930
... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.413399
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.508824
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.417374
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.472965
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.634831
proj <- addCellColData(ArchRProj = proj, data = df_label$predictedGroup_RNA2ATAC,
cells = rownames(df_label), name = "predictedGroup_RNA2ATAC", force = TRUE)
#proj <- addCellColData(ArchRProj = proj, data = df_label$Celltype1,
# cells = rownames(df_label), name = "Celltype1", force = TRUE)
proj
getCellColData(proj)
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ... Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(30): Sample TSSEnrichment ... FRIP predictedGroup_RNA2ATAC numberOfCells(1): 75955 medianTSS(1): 23.946 medianFrags(1): 16376
DataFrame with 75955 rows and 30 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58 25.310
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69 10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69 17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69 11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69 13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69 30.716
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 13881 45719
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 243 1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 446 1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 283 1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 318 1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 667 2131
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 3927 0.314804 1
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 138 0.156816 1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 268 0.235505 1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 208 0.194057 1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 164 0.192780 1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 170 0.332449 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.627884 6400 44607
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 9.203030 721 330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.428157 438 1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 4.676420 681 581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 7.410853 707 387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.510368 150 2122
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 72615 21608 0
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 3367 2316 0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 3346 1530 0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 3298 2036 0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 3255 2161 0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 3205 933 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.7666667 0.0270399
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.2444444 0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.0222222 0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.0000000 0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.3555556 0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.6444444 0.0265211
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse DorsalHorn C20
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse DorsalHorn C24
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC C20 4.86103 Micro
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C24 3.52724 Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C1 3.52453 Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C1 3.51825 Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C24 3.51255 Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C24 3.50583 Oligo
predictedGroup_RNA2ATACCo ReadsInPeaks
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen 63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen 67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1 52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen 66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Ependymal.cells 98301
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1 2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia 3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia 2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1 3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1 4068
FRIP predictedGroup_RNA2ATAC
<numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.398623 midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.456443 midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.356678 GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.457930 midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.676930 Ependymal.cells
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.413399 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.508824 Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.417374 Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.472965 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.634831 Oligo.1
table(proj$Celltype1)
table(proj$predictedGroup_RNA2ATACCo)
table(proj$predictedGroup_RNA2ATAC)
Astrocyte Ex-Cpne4 Ex-Maf Ex-Prkcg Ex-Reln Ex-Rreb1
13355 1330 2134 523 3426 5
Ex-Sox5 Inh-Adamts5 Inh-Cdh3 Inh-Npy Inh-Pdyn Inh-Rorb
5592 2296 1073 405 1308 1105
Meninges Micro midVent Oligo OPC Schwann
603 3284 1394 33256 781 4085
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells GABA1
2417 10926 788 951 1077
GABA2 GABA3 GABA4 GABA5 GLUT1
1606 405 1786 1310 564
GLUT10 GLUT11 GLUT2 GLUT3 GLUT4
289 8 2848 1604 806
GLUT5 GLUT6 GLUT7 GLUT8 GLUT9
5 2892 2135 1586 56
Meninges Microglia midVen Mural Oligo.1
2 2328 1614 736 32624
Oligo.2 OPC
1244 3348
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells GABA1
2417 10926 788 951 1078
GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2
64 1545 376 967 795
GABA5 GLUT1 GLUT10 GLUT11 GLUT2
1320 1092 431 39 2452
GLUT3 GLUT4 GLUT5 GLUT6 GLUT7
1945 341 992 2195 2283
GLUT8 GLUT9 Meninges Microglia midVen
1157 1 2 2328 1518
Mural Oligo.1 Oligo.2 OPC
736 32624 1244 3348
## subset to cells with integrated labels
idxPass <- which(!is.na(proj$predictedGroup_RNA2ATACCo) &
proj$predictedGroup_RNA2ATACCo %ni% c('Drop', 'NA.', 'TH')) # too few cluster
#impute weights dropped, 'cell-x-cell' matrix
cellsPass <- proj$cellNames[idxPass]
proj = subsetCells(ArchRProj = proj, cellNames = cellsPass)
proj
getCellColData(proj)
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ... Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(29): Sample TSSEnrichment ... ReadsInPeaks FRIP numberOfCells(1): 75955 medianTSS(1): 23.946 medianFrags(1): 16376
DataFrame with 75955 rows and 29 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58 25.310
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69 10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69 17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69 11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69 13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69 30.716
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 13881 45719
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 243 1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 446 1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 283 1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 318 1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 667 2131
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 3927 0.314804 1
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 138 0.156816 1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 268 0.235505 1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 208 0.194057 1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 164 0.192780 1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 170 0.332449 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.627884 6400 44607
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 9.203030 721 330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.428157 438 1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 4.676420 681 581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 7.410853 707 387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.510368 150 2122
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 72615 21608 0
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 3367 2316 0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 3346 1530 0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 3298 2036 0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 3255 2161 0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 3205 933 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.7666667 0.0270399
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.2444444 0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.0222222 0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.0000000 0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.3555556 0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.6444444 0.0265211
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse DorsalHorn C20
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse DorsalHorn C24
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC C20 4.86103 Ependymal.cells
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C24 3.52724 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C1 3.52453 Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C1 3.51825 Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C24 3.51255 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C24 3.50583 Oligo.1
predictedGroup_RNA2ATACCo ReadsInPeaks
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen 63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen 67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1 52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen 66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Ependymal.cells 98301
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1 2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia 3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia 2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1 3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1 4068
FRIP
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.398623
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.456443
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.356678
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.457930
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.676930
... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.413399
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.508824
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.417374
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.472965
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.634831
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Sample", embedding = "UMAPH200")
p2 <- plotEmbedding(proj, colorBy = "cellColData",
name = "Celltype1", embedding = "UMAPH200")
p3 <- plotEmbedding(proj, colorBy = "cellColData",
name = "predictedGroup_RNA2ATACCo", embedding = "UMAPH200")
p4 <- plotEmbedding(proj, colorBy = "cellColData",
name = "predictedGroup_RNA2ATAC", embedding = "UMAPH200")
ggAlignPlots(p1, p2, p3, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f3940f522-Date-2023-01-31_Time-21-54-23.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f3940f522-Date-2023-01-31_Time-21-54-23.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f7a2bb031-Date-2023-01-31_Time-21-54-42.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f7a2bb031-Date-2023-01-31_Time-21-54-42.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f66db3091-Date-2023-01-31_Time-21-54-45.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f66db3091-Date-2023-01-31_Time-21-54-45.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f2faf7889-Date-2023-01-31_Time-21-54-48.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f2faf7889-Date-2023-01-31_Time-21-54-48.log
proj <- addImputeWeights(proj, reducedDims = "HarmonyI200")
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-5b3435d52c362-Date-2023-01-30_Time-10-51-35.log If there is an issue, please report to github with logFile! 2023-01-30 10:51:38 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
## Neuron vs. Glia markers
markerGenes1 <- c('SRRM3',#Neurons
'MYT1L',#Neurons
'RBFOX3'#Neurons
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e6bcd96e4-Date-2022-10-21_Time-10-08-59.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:09:01 : Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e6bcd96e4-Date-2022-10-21_Time-10-08-59.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('ITGB4',#Astrocyte1
'GFAP',#Astrocyte1
'SLC7A10',#Astrocyte2
'PDZRN4'#Astrocyte2
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-5b3434dab729e-Date-2023-01-30_Time-10-38-51.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2023-01-30 10:39:43 : Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-5b3434dab729e-Date-2023-01-30_Time-10-38-51.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('RFX2'#Ependymal
# 'DNAH12'#Ependymal
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e227ae1be-Date-2022-10-21_Time-10-22-57.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:22:58 : Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e227ae1be-Date-2022-10-21_Time-10-22-57.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Error in x + guides(color = FALSE, fill = FALSE): non-numeric argument to binary operator
Traceback:
1. lapply(p, function(x) {
. x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) +
. theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(),
. axis.ticks.x = element_blank(), axis.text.y = element_blank(),
. axis.ticks.y = element_blank())
. })
2. lapply(p, function(x) {
. x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) +
. theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(),
. axis.ticks.x = element_blank(), axis.text.y = element_blank(),
. axis.ticks.y = element_blank())
. })
3. FUN(X[[i]], ...)
## Neuron vs. Glia markers
markerGenes1 <- c('LAMA2',#Meninges
'BICC1'#Meninges
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-5b34352a6a59c-Date-2023-01-30_Time-10-40-56.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2023-01-30 10:41:19 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-5b34352a6a59c-Date-2023-01-30_Time-10-40-56.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('Flt1',#Endothelial
'Notch3'#Mural
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-41a44169b6b4-Date-2023-02-15_Time-10-12-05.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneIntegrationMatrix Getting Matrix Values... 2023-02-15 10:12:13 : Warning message in mclapply(..., mc.cores = threads, mc.preschedule = preschedule): “12 function calls resulted in an error”
Error in .safelapply(seq_along(cellNamesList), function(x) {:
Error Found Iteration 1 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 2 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 3 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 4 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 5 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 6 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 7 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 8 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 9 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 10 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 11 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 12 :
[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Traceback:
1. plotEmbedding(ArchRProj = proj, colorBy = "GeneIntegrationMatrix",
. name = markerGenes1, embedding = "UMAPH200")
2. .getMatrixValues(ArchRProj = ArchRProj, name = name, matrixName = colorBy,
. log2Norm = FALSE, threads = threads, logFile = logFile)
3. .safelapply(seq_along(cellNamesList), function(x) {
. if (getArchRVerbose())
. message(x, " ", appendLF = FALSE)
. valuesx <- tryCatch({
. o <- h5closeAll()
. ArrowFile <- getSampleColData(ArchRProj)[names(cellNamesList)[x],
. "ArrowFiles"]
. valuesx <- .getMatFromArrow(ArrowFile = ArrowFile, featureDF = featureDF,
. binarize = FALSE, useMatrix = matrixName, cellNames = cellNamesList[[x]],
. threads = 1)
. colnames(valuesx) <- cellNamesList[[x]]
. valuesx
. }, error = function(e) {
. errorList <- list(x = x, ArrowFile = ArrowFile, ArchRProj = ArchRProj,
. cellNames = ArchRProj$cellNames, cellNamesList = cellNamesList,
. featureDF = featureDF)
. .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,
. logFile = logFile)
. })
. valuesx
. }, threads = threads) %>% Reduce("cbind", .)
4. Reduce("cbind", .)
5. .safelapply(seq_along(cellNamesList), function(x) {
. if (getArchRVerbose())
. message(x, " ", appendLF = FALSE)
. valuesx <- tryCatch({
. o <- h5closeAll()
. ArrowFile <- getSampleColData(ArchRProj)[names(cellNamesList)[x],
. "ArrowFiles"]
. valuesx <- .getMatFromArrow(ArrowFile = ArrowFile, featureDF = featureDF,
. binarize = FALSE, useMatrix = matrixName, cellNames = cellNamesList[[x]],
. threads = 1)
. colnames(valuesx) <- cellNamesList[[x]]
. valuesx
. }, error = function(e) {
. errorList <- list(x = x, ArrowFile = ArrowFile, ArchRProj = ArchRProj,
. cellNames = ArchRProj$cellNames, cellNamesList = cellNamesList,
. featureDF = featureDF)
. .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,
. logFile = logFile)
. })
. valuesx
. }, threads = threads)
6. stop(errorMsg)
## Neuron vs. Glia markers
markerGenes1 <- c('MYO1F',#Microglia
'PALD1' #Microglia
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e28130342-Date-2022-10-21_Time-10-22-07.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:22:10 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e28130342-Date-2022-10-21_Time-10-22-07.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('QDPR',#Oligo1
'DPY19L1'#Oligo2
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7ede42222-Date-2022-10-21_Time-10-21-37.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:21:38 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7ede42222-Date-2022-10-21_Time-10-21-37.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('MEGF11',#OPC
'TNR'#OPC
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e374b11be-Date-2022-10-21_Time-10-21-08.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:21:11 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e374b11be-Date-2022-10-21_Time-10-21-08.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('MPZ',#Schwann
'PMP22'#Schwann
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e2195493-Date-2022-10-21_Time-10-13-35.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:13:38 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e2195493-Date-2022-10-21_Time-10-13-35.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Excitatory vs. Inhibitory markers
markerGenes1 <- c('SLC17A6','FSTL4', # Excitatory
'SLC32A1','PAX2' # Inhibitory
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e918fa13-Date-2022-10-21_Time-10-14-07.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:14:10 : Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e918fa13-Date-2022-10-21_Time-10-14-07.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1 <- c('GFRA1',
'CRHR2',
'COL13A1',
'NMUR2',
# 'TAC3',
'NMU',
'COL5A2',
'GHR',
'COL24A1',
'NMBR',
'TAC1',
# 'ANOS1',
'FSTL4',
'ADARB2',
'MAF',
'ST8SIA6',
'MAFA',
'NTNG1',
'ADAMTS16',
'TLL2',
'OTOGL'
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e7efe2284-Date-2022-10-21_Time-10-15-05.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:15:08 : Plotting Embedding 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e7efe2284-Date-2022-10-21_Time-10-15-05.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Inhibitory Nuerons
markerGenes1 <- c('MASP1',
'RREB1',
'NPY',
'MET',
'PTN',
'PDYN'
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights No imputeWeights found, returning NULL ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e4c3c03a7-Date-2022-10-21_Time-10-17-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-21 10:17:20 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e4c3c03a7-Date-2022-10-21_Time-10-17-19.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200", embedding = "UMAPH200")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPH200")
ggAlignPlots(p1, p2, type = "h")
proj$logNFrags = log10(proj$nFrags)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "logNFrags", embedding = "UMAPH200")
ggAlignPlots(p1, p3, type = "h")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "TSSEnrichment", embedding = "UMAPH200")
ggAlignPlots(p1, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e842a4ec-Date-2022-10-21_Time-10-18-11.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e842a4ec-Date-2022-10-21_Time-10-18-11.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e51d6d3b8-Date-2022-10-21_Time-10-18-12.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e51d6d3b8-Date-2022-10-21_Time-10-18-12.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7ef066510-Date-2022-10-21_Time-10-18-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7ef066510-Date-2022-10-21_Time-10-18-19.log
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e27ef7ad6-Date-2022-10-21_Time-10-18-26.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e27ef7ad6-Date-2022-10-21_Time-10-18-26.log
proj = saveArchRProject(proj)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
library(BSgenome.Mmusculus.UCSC.mm10)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘XVector’
The following object is masked from ‘package:purrr’:
compact
The following object is masked from ‘package:plyr’:
compact
Attaching package: ‘Biostrings’
The following object is masked from ‘package:grid’:
pattern
The following object is masked from ‘package:base’:
strsplit
Loading required package: rtracklayer
# make group coverage, call peaks, and
proj<-addGroupCoverages(proj, groupBy="predictedGroup_RNA2ATAC",
minReplicates = 5, maxReplicates = 11, force = TRUE,
minCells = 40, maxCells = 1000)
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-2d9e2ec554f6-Date-2023-02-01_Time-21-48-53.log If there is an issue, please report to github with logFile! Astrocyte.1 (1 of 29) : CellGroups N = 11 Astrocyte.2 (2 of 29) : CellGroups N = 11 Endothelial (3 of 29) : CellGroups N = 11 Ependymal.cells (4 of 29) : CellGroups N = 11 GABA1 (5 of 29) : CellGroups N = 11 GABA2_1 (6 of 29) : CellGroups N = 5 GABA2_2 (7 of 29) : CellGroups N = 11 GABA3 (8 of 29) : CellGroups N = 5 GABA4_1 (9 of 29) : CellGroups N = 11 GABA4_2 (10 of 29) : CellGroups N = 11 GABA5 (11 of 29) : CellGroups N = 11 GLUT1 (12 of 29) : CellGroups N = 11 GLUT2 (13 of 29) : CellGroups N = 11 GLUT3 (14 of 29) : CellGroups N = 11 GLUT4 (15 of 29) : CellGroups N = 5 GLUT5 (16 of 29) : CellGroups N = 11 GLUT6 (17 of 29) : CellGroups N = 11 GLUT7 (18 of 29) : CellGroups N = 11 GLUT8 (19 of 29) : CellGroups N = 11 GLUT9 (20 of 29) : CellGroups N = 5 GLUT10 (21 of 29) : CellGroups N = 6 GLUT11 (22 of 29) : CellGroups N = 5 Meninges (23 of 29) : CellGroups N = 5 Microglia (24 of 29) : CellGroups N = 11 midVen (25 of 29) : CellGroups N = 11 Mural (26 of 29) : CellGroups N = 11 Oligo.1 (27 of 29) : CellGroups N = 11 Oligo.2 (28 of 29) : CellGroups N = 11 OPC (29 of 29) : CellGroups N = 11 2023-02-01 21:50:18 : Creating Coverage Files!, 1.419 mins elapsed. 2023-02-01 21:50:18 : Batch Execution w/ safelapply!, 1.419 mins elapsed. 2023-02-01 23:11:56 : Adding Kmer Bias to Coverage Files!, 83.04 mins elapsed. 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ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-2d9e2ec554f6-Date-2023-02-01_Time-21-48-53.log
proj = saveArchRProject(proj)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# call peaks
proj<-addReproduciblePeakSet(proj, groupBy = "predictedGroup_RNA2ATAC", reproducibility = "(n + 1)/2",
plot = FALSE, genomeSize = 2.7e9)
Searching For MACS2.. Found with $path! ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-2d9e276e9063-Date-2023-02-01_Time-23-47-42.log If there is an issue, please report to github with logFile! Calling Peaks with Macs2 2023-02-01 23:47:44 : Peak Calling Parameters!, 0.027 mins elapsed.
Group nCells nCellsUsed nReplicates nMin nMax
Astrocyte.1 Astrocyte.1 2417 2295 11 122 293
Astrocyte.2 Astrocyte.2 10926 9492 11 677 1000
Endothelial Endothelial 788 736 11 57 85
Ependymal.cells Ependymal.cells 951 903 11 56 113
GABA1 GABA1 1078 1015 11 64 120
GABA2_1 GABA2_1 64 63 5 40 40
GABA2_2 GABA2_2 1545 1453 11 102 155
GABA3 GABA3 376 376 5 43 97
GABA4_1 GABA4_1 967 916 11 61 107
GABA4_2 GABA4_2 795 749 11 48 94
GABA5 GABA5 1320 1248 11 78 151
GLUT1 GLUT1 1092 1032 11 70 131
GLUT2 GLUT2 2452 2297 11 156 279
GLUT3 GLUT3 1945 1826 11 127 216
GLUT4 GLUT4 341 341 5 65 69
GLUT5 GLUT5 992 928 11 64 109
GLUT6 GLUT6 2195 2058 11 147 236
GLUT7 GLUT7 2283 2153 11 139 244
GLUT8 GLUT8 1157 1082 11 78 120
GLUT9 GLUT9 1 1 5 1 1
GLUT10 GLUT10 431 431 6 42 209
GLUT11 GLUT11 39 39 5 21 27
Meninges Meninges 2 2 5 2 2
Microglia Microglia 2328 2185 11 152 244
midVen midVen 1518 1430 11 98 166
Mural Mural 736 693 11 45 81
Oligo.1 Oligo.1 32624 11000 11 1000 1000
Oligo.2 Oligo.2 1244 1175 11 73 139
OPC OPC 3348 3168 11 202 369
maxPeaks
Astrocyte.1 150000
Astrocyte.2 150000
Endothelial 150000
Ependymal.cells 150000
GABA1 150000
GABA2_1 31500
GABA2_2 150000
GABA3 150000
GABA4_1 150000
GABA4_2 150000
GABA5 150000
GLUT1 150000
GLUT2 150000
GLUT3 150000
GLUT4 150000
GLUT5 150000
GLUT6 150000
GLUT7 150000
GLUT8 150000
GLUT9 500
GLUT10 150000
GLUT11 19500
Meninges 1000
Microglia 150000
midVen 150000
Mural 150000
Oligo.1 150000
Oligo.2 150000
OPC 150000
2023-02-01 23:47:44 : Batching Peak Calls!, 0.028 mins elapsed. 2023-02-01 23:47:46 : Batch Execution w/ safelapply!, 0 mins elapsed. 2023-02-02 01:28:26 : Identifying Reproducible Peaks!, 100.729 mins elapsed. 2023-02-02 01:30:36 : Creating Union Peak Set!, 102.887 mins elapsed. Converged after 9 iterations! 2023-02-02 01:30:54 : Finished Creating Union Peak Set (518748)!, 103.194 mins elapsed.
# add peak counts matrix
proj <- addPeakMatrix(proj)
ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-1c87954e054fd-Date-2023-02-09_Time-12-36-27.log If there is an issue, please report to github with logFile! 2023-02-09 12:36:28 : Batch Execution w/ safelapply!, 0 mins elapsed. Overriding previous entry for ReadsInPeaks Overriding previous entry for FRIP ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-1c87954e054fd-Date-2023-02-09_Time-12-36-27.log
BiocManager::install("JASPAR2020")
library(JASPAR2020)
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.r-project.org
Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10)
Installing package(s) 'JASPAR2020'
Updating HTML index of packages in '.Library'
Making 'packages.html' ...
done
Old packages: 'brew', 'clue', 'commonmark', 'cpp11', 'curl', 'data.table',
'desc', 'devtools', 'digest', 'evaluate', 'gargle', 'gert', 'gh', 'gitcreds',
'haven', 'isoband', 'lifecycle', 'nlme', 'openssl', 'pracma', 'ragg',
'RCurl', 'readr', 'rmarkdown', 'RSQLite', 'sys', 'testthat', 'tidyselect',
'tinytex', 'vroom', 'xfun', 'XML', 'yaml', 'zip'
# add motif enrichment matrix
proj <- addMotifAnnotations(ArchRProj = proj, motifSet = "encode", name = "Motif",logFile = createLogFile("addMotifAnnotations"), species = getGenome(proj), force = TRUE)
ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-1c879242927da-Date-2023-02-09_Time-11-47-15.log If there is an issue, please report to github with logFile! peakAnnotation name already exists! Overriding. 2023-02-09 11:47:15 : Gettting Motif Set, Species : BSgenome.Mmusculus.UCSC.mm10, 0.004 mins elapsed. 2023-02-09 11:47:23 : Finding Motif Positions with motifmatchr!, 0.142 mins elapsed. 2023-02-09 12:32:55 : All Motifs Overlap at least 1 peak!, 45.668 mins elapsed. 2023-02-09 12:32:55 : Creating Motif Overlap Matrix, 45.668 mins elapsed. 2023-02-09 12:33:12 : Finished Getting Motif Info!, 45.957 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-1c879242927da-Date-2023-02-09_Time-11-47-15.log
# # add motif deviations matrix
proj <- addBgdPeaks(proj, force = TRUE)
Identifying Background Peaks!
#not run
proj <- addDeviationsMatrix(proj, peakAnnotation = "Motif", force = TRUE)
Identifying Background Peaks! ArchR logging to : ArchRLogs/ArchR-addDeviationsMatrix-206be1585f45d-Date-2023-02-10_Time-09-45-41.log If there is an issue, please report to github with logFile!
NULL
as(<lgCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "dMatrix") instead 2023-02-10 09:46:06 : Batch Execution w/ safelapply!, 0 mins elapsed. ########### 2023-02-10 20:57:46 : Completed Computing Deviations!, 672.082 mins elapsed. ########### ArchR logging successful to : ArchRLogs/ArchR-addDeviationsMatrix-206be1585f45d-Date-2023-02-10_Time-09-45-41.log
proj = saveArchRProject(proj)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
plotVarDev <- getVarDeviations(proj, name = "MotifMatrix")
# add co-accessibility matrix
proj <- addCoAccessibility(proj, reducedDims = "HarmonyI200", dimsToUse = 1:30,
scaleDims = TRUE, corCutOff = 0.75, k = 100,
knnIteration = 500, overlapCutoff = 0.8,
maxDist = 1e+05, scaleTo = 10^4, log2Norm = TRUE)
ArchR logging to : ArchRLogs/ArchR-addCoAccessibility-44b7e20e09826-Date-2022-10-21_Time-09-13-02.log If there is an issue, please report to github with logFile! 2022-10-21 09:13:02 : Computing KNN, 0.003 mins elapsed. 2022-10-21 09:13:03 : Identifying Non-Overlapping KNN pairs, 0.011 mins elapsed. 2022-10-21 09:13:07 : Identified 498 Groupings!, 0.076 mins elapsed. 2022-10-21 09:14:08 : Computing Co-Accessibility chr1 (1 of 20), 1.102 mins elapsed. 2022-10-21 09:14:54 : Computing Co-Accessibility chr2 (2 of 20), 1.87 mins elapsed. 2022-10-21 09:15:52 : Computing Co-Accessibility chr3 (3 of 20), 2.833 mins elapsed. 2022-10-21 09:16:35 : Computing Co-Accessibility chr4 (4 of 20), 3.557 mins elapsed. 2022-10-21 09:17:27 : Computing Co-Accessibility chr5 (5 of 20), 4.413 mins elapsed. 2022-10-21 09:18:18 : Computing Co-Accessibility chr6 (6 of 20), 5.275 mins elapsed. 2022-10-21 09:19:01 : Computing Co-Accessibility chr7 (7 of 20), 5.987 mins elapsed. 2022-10-21 09:19:52 : Computing Co-Accessibility chr8 (8 of 20), 6.828 mins elapsed. 2022-10-21 09:20:30 : Computing Co-Accessibility chr9 (9 of 20), 7.467 mins elapsed. 2022-10-21 09:21:18 : Computing Co-Accessibility chr10 (10 of 20), 8.26 mins elapsed. 2022-10-21 09:22:01 : Computing Co-Accessibility chr11 (11 of 20), 8.977 mins elapsed. 2022-10-21 09:23:01 : Computing Co-Accessibility chr12 (12 of 20), 9.984 mins elapsed. 2022-10-21 09:23:40 : Computing Co-Accessibility chr13 (13 of 20), 10.635 mins elapsed. 2022-10-21 09:24:19 : Computing Co-Accessibility chr14 (14 of 20), 11.277 mins elapsed. 2022-10-21 09:24:53 : Computing Co-Accessibility chr15 (15 of 20), 11.848 mins elapsed. 2022-10-21 09:25:27 : Computing Co-Accessibility chr16 (16 of 20), 12.417 mins elapsed. 2022-10-21 09:26:00 : Computing Co-Accessibility chr17 (17 of 20), 12.961 mins elapsed. 2022-10-21 09:26:38 : Computing Co-Accessibility chr18 (18 of 20), 13.598 mins elapsed. 2022-10-21 09:27:10 : Computing Co-Accessibility chr19 (19 of 20), 14.134 mins elapsed. 2022-10-21 09:27:40 : Computing Co-Accessibility chrX (20 of 20), 14.635 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addCoAccessibility-44b7e20e09826-Date-2022-10-21_Time-09-13-02.log
markerGenes <- c('ITGB4',#Astrocyte1
'GFAP',#Astrocyte1
'SLC7A10',#Astrocyte2
'PDZRN4'#Astrocyte2
)
p <- plotBrowserTrack(
ArchRProj = proj,
groupBy = "ClustersH200",
geneSymbol = markerGenes,
upstream = 50000,
downstream = 50000,
loops = getCoAccessibility(proj)
)
ArchR logging to : ArchRLogs/ArchR-plotBrowserTrack-44b7e797f5dd7-Date-2022-10-21_Time-10-04-51.log If there is an issue, please report to github with logFile! 2022-10-21 10:04:51 : Validating Region, 0.009 mins elapsed.
GRanges object with 4 ranges and 2 metadata columns:
seqnames ranges strand | gene_id symbol
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr11 115974725-116008411 + | 192897 Itgb4
[2] chr11 102887336-102897200 - | 14580 Gfap
[3] chr7 35186385-35201111 + | 53896 Slc7a10
[4] chr15 92396810-92771819 + | 239618 Pdzrn4
-------
seqinfo: 21 sequences from mm10 genome
2022-10-21 10:04:51 : Adding Bulk Tracks (1 of 4), 0.011 mins elapsed. 2022-10-21 10:05:17 : Adding Feature Tracks (1 of 4), 0.437 mins elapsed. 2022-10-21 10:05:17 : Adding Loop Tracks (1 of 4), 0.438 mins elapsed. 2022-10-21 10:05:21 : Adding Gene Tracks (1 of 4), 0.507 mins elapsed. 2022-10-21 10:05:21 : Plotting, 0.51 mins elapsed. 2022-10-21 10:05:25 : Adding Bulk Tracks (2 of 4), 0.574 mins elapsed. 2022-10-21 10:05:45 : Adding Feature Tracks (2 of 4), 0.899 mins elapsed. 2022-10-21 10:05:45 : Adding Loop Tracks (2 of 4), 0.9 mins elapsed. 2022-10-21 10:05:49 : Adding Gene Tracks (2 of 4), 0.969 mins elapsed. 2022-10-21 10:05:50 : Plotting, 0.989 mins elapsed. 2022-10-21 10:05:54 : Adding Bulk Tracks (3 of 4), 1.053 mins elapsed. 2022-10-21 10:06:13 : Adding Feature Tracks (3 of 4), 1.379 mins elapsed. 2022-10-21 10:06:13 : Adding Loop Tracks (3 of 4), 1.38 mins elapsed. 2022-10-21 10:06:23 : Adding Gene Tracks (3 of 4), 1.543 mins elapsed. 2022-10-21 10:06:23 : Plotting, 1.547 mins elapsed. 2022-10-21 10:06:28 : Adding Bulk Tracks (4 of 4), 1.625 mins elapsed. 2022-10-21 10:06:46 : Adding Feature Tracks (4 of 4), 1.93 mins elapsed. 2022-10-21 10:06:46 : Adding Loop Tracks (4 of 4), 1.93 mins elapsed. 2022-10-21 10:06:48 : Adding Gene Tracks (4 of 4), 1.956 mins elapsed. 2022-10-21 10:06:48 : Plotting, 1.959 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-plotBrowserTrack-44b7e797f5dd7-Date-2022-10-21_Time-10-04-51.log
names(attributes(proj)$reducedDims)
proj = saveArchRProject(ArchRProj = proj)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
getAvailableMatrices(proj)
proj <- addCellColData(ArchRProj = proj, data = proj$predictedGroup_RNA2ATAC,
cells = rownames(getCellColData(proj)), name = "FINAL_GROUP_LABEL", force = TRUE)
names(getCellColData(proj))
getCellColData(proj)
DataFrame with 75955 rows and 31 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58 25.310
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69 10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69 17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69 11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69 13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69 30.716
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 13881 45719
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 243 1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 446 1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 283 1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 318 1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 667 2131
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 3927 0.314804 1
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 138 0.156816 1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 268 0.235505 1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 208 0.194057 1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 164 0.192780 1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 170 0.332449 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.627884 6400 44607
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 9.203030 721 330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 1.428157 438 1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 4.676420 681 581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 7.410853 707 387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.510368 150 2122
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 72615 21608 0
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 3367 2316 0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 3346 1530 0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 3298 2036 0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 3255 2161 0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 3205 933 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.7666667 0.0270399
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.2444444 0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.0222222 0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.0000000 0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.3555556 0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.6444444 0.0265211
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse DorsalHorn C20
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse DorsalHorn C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse DorsalHorn C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse DorsalHorn C24
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC C20 4.86103 Micro
... ... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC C24 3.52724 Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG C1 3.52453 Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA C1 3.51825 Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT C24 3.51255 Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG C24 3.50583 Oligo
predictedGroup_RNA2ATACCo ReadsInPeaks
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen 63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen 67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1 52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen 66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Ependymal.cells 98301
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1 2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia 3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia 2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1 3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1 4068
FRIP predictedGroup_RNA2ATAC
<numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.398623 midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.456443 midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.356678 GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.457930 midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC 0.676930 Ependymal.cells
... ... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC 0.413399 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG 0.508824 Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA 0.417374 Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT 0.472965 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG 0.634831 Oligo.1
FINAL_GROUP_LABEL
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Ependymal.cells
... ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Oligo.1
table(proj$predictedGroup_RNA2ATAC)
table(proj$FINAL_GROUP_LABEL)
proj = saveArchRProject(ArchRProj = proj)
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells GABA1
2417 10926 788 951 1078
GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2
64 1545 376 967 795
GABA5 GLUT1 GLUT10 GLUT11 GLUT2
1320 1092 431 39 2452
GLUT3 GLUT4 GLUT5 GLUT6 GLUT7
1945 341 992 2195 2283
GLUT8 GLUT9 Meninges Microglia midVen
1157 1 2 2328 1518
Mural Oligo.1 Oligo.2 OPC
736 32624 1244 3348
Astrocyte.1 Astrocyte.2 Endothelial Ependymal.cells GABA1
2417 10926 788 951 1078
GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2
64 1545 376 967 795
GABA5 GLUT1 GLUT10 GLUT11 GLUT2
1320 1092 431 39 2452
GLUT3 GLUT4 GLUT5 GLUT6 GLUT7
1945 341 992 2195 2283
GLUT8 GLUT9 Meninges Microglia midVen
1157 1 2 2328 1518
Mural Oligo.1 Oligo.2 OPC
736 32624 1244 3348
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
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